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Shao-Ma-Zhi-Jing granules alleviate Tourette Syndrome by modulating the cAMP/PI3K/AKT/NF-κB signaling pathway, T cell differentiation, microglia, and gut microbiota.

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The authors' code

Python · 947 lines · 30 KB · GPL-3.0

  1. #!/usr/bin/env python
  2. # MinPath
  3. # developed by Yuzhen Ye ([email hidden])
  4. # Indiana University, Bloomington
  6. # what's new in version 1.2 (released on Oct 19, 2010)
  7. # MinPath1.2 works on any pathway system
  8. # what you need: a pathway-function mapping file (e.g, data/ec2path), and your input file
  10. # what's new in version 1.1 (released on July 31, 2010)
  11. # * numpy independent
  12. # * add detailed output of ko assignments to each pathway
  14. import sys
  15. import os
  16. import re
  17. import operator
  18. import math
  20. # LJM Add location to minpath directory
  21. import subprocess
  22. minpath=os.path.join(os.path.dirname(os.path.abspath(__file__)),"MinPath")
  24. # LJM Remove search for minpath directory
  25. #minpath = os.environ.get('MinPath')
  26. #path0 = "/home/yye/Pathways/MinPath"
  27. #if minpath or os.path.exists(path0):
  28. # if os.path.exists(path0):
  29. # minpath = path0
  30. #else:
  31. # sys.exit("Environment variable MinPath not set")
  33. keggPath0, seedPath0, mapPath0, glpsol0 = minpath + "/data", minpath + "/data", minpath + "/data", minpath + "/glpk-4.6/examples/glpsol"
  35. # LJM Check if glpsol is installed globally, if so use this version instead
  36. glpsol_global=None
  37. paths = os.environ["PATH"].split(os.pathsep)
  38. for path in paths:
  39. fullexe = os.path.join(path,"glpsol")
  40. if os.path.exists(fullexe):
  41. if os.access(fullexe,os.X_OK):
  42. glpsol_global=fullexe
  43. break
  45. if not glpsol_global is None:
  46. # check if the global install is working properly
  47. try:
  48. stdout=subprocess.check_output([glpsol_global,"--help"])
  49. except (EnvironmentError,subprocess.CalledProcessError):
  50. glpsol_global=None
  52. # if the global install is operating as expected, then use this version
  53. if not glpsol_global is None:
  54. glpsol0=glpsol_global
  56. # this function returns a string from a group of items
  57. def get_string(*items):
  58. return " ".join(str(i) for i in items)
  60. def intmatrix(dim1, dim2):
  61. mat = []
  62. for i in range(dim1):
  63. tmp = [0] * dim2
  64. mat.append(tmp)
  66. return mat
  68. class MinPath:
  70. def __init__(self, whichdb = "KEGG", pathdir="", getgene = False, givenspe = "", mapfile = ""):
  71. self.whichDB = whichdb
  72. self.speID = givenspe
  73. global keggPath0
  74. global seedPath0
  75. global mapPath0
  76. if pathdir == "":
  77. if whichdb == "KEGG":
  78. self.dataDir = keggPath0
  79. elif whichdb == "SEED":
  80. self.dataDir = seedPath0
  81. else:
  82. self.dataDir = mapPath0
  83. else:
  84. self.dataDir = pathdir
  85. self.famTot = 0
  86. self.pathwayTot = 0
  87. self.famList = []
  88. self.famID = []
  89. self.famName = []
  90. self.famCount = []
  91. self.fam2Path = []
  92. self.pathList = []
  93. self.pathName = []
  94. self.path2Fam = []
  95. self.path2FamUni = []
  96. self.orgList = []
  97. self.orgGene2Fam = []
  98. self.orgGeneList = []
  99. self.famMapped = []
  100. self.pathMapped = []
  102. if whichdb == "SEED":
  103. print("now get SEED")
  104. fig2ssfile = self.dataDir + "/figfam_subsystem.dat"
  105. self.ReadFigSubsytem(fig2ssfile)
  106. elif whichdb == "KEGG":
  107. pathfile = self.dataDir + "/map_title.tab"
  108. self.ReadKEGGPath(pathfile)
  110. kofile = self.dataDir + "/ko"
  111. self.ReadKO(kofile, getgene, givenspe) #KO: KEGG family
  112. else:
  113. if os.path.exists(mapfile):
  114. print("mapfile", mapfile)
  115. self.ReadAnyMap(mapfile)
  116. elif os.path.exists(self.dataDir + "/" + os.path.basename(mapfile)):
  117. print("file: ", self.dataDir + "/" + os.path.basename(mapfile))
  118. self.ReadAnyMap(self.dataDir + "/" + os.path.basename(mapfile))
  119. else:
  120. sys.exit("file " + mapfile + " not found")
  122. self.CheckUniqueFam()
  124. def GetPathList(self):
  125. return self.pathList;
  127. def GetPathName(self):
  128. return self.pathName;
  130. def ReadAnyMap(self, mapfile):
  131. try:
  132. file = open(mapfile, "rt")
  133. except IOError:
  134. print("open file %s error" % mapfile)
  136. for aline in file:
  137. if aline[0] == '#':
  138. continue
  139. subs = aline.strip().split()
  140. if len(subs) < 2:
  141. continue
  142. path = subs[0]
  143. for fam in subs[1:]:
  144. if path in self.pathName:
  145. pathidx = self.pathName.index(path)
  146. else:
  147. pathidx = len(self.pathList)
  148. self.pathList.append(str(pathidx + 1))
  149. self.pathName.append(path)
  150. self.path2Fam.append([])
  151. if fam in self.famID:
  152. famidx = self.famID.index(fam)
  153. else:
  154. famidx = len(self.famList)
  155. self.famList.append(str(famidx + 1))
  156. self.famName.append(fam)
  157. self.famID.append(fam)
  158. self.fam2Path.append([])
  159. if famidx not in self.path2Fam[pathidx]:
  160. self.path2Fam[pathidx].append(famidx)
  161. self.fam2Path[famidx].append(pathidx)
  162. #same path & fun could be listed multiple times
  164. self.famTot = len(self.famList)
  165. self.pathTot = len(self.pathList)
  166. print("total family", self.famTot, " pathway", self.pathTot)
  167. #for idx in range(self.pathTot):
  168. # print "path", self.pathName[idx], " include fam", len(self.path2Fam[idx])
  170. #read SEED figfam to subsytem mapping
  171. def ReadFigSubsytem(self, fig2ssfile):
  172. print("fig2ssfile=%s" % fig2ssfile)
  173. try:
  174. file = open(fig2ssfile, "rt")
  175. except IOError:
  176. print("open file %s error" % fig2ssfile)
  177. for aline in file:
  178. aline = aline.strip()
  179. #note: in seed, a "family" (or "function") can have multiple FIG "sub"families
  180. #the families and the subsytems have names, but not codes
  181. #(subfam, fam, path) = aline.split('\t')
  182. cols = aline.split('\t')
  183. if len(cols) < 3:
  184. continue # skip the families that have NO subsystems assignment
  185. fam = cols[1]
  186. if fam in self.famName:
  187. famidx = self.famName.index(fam)
  188. else:
  189. famidx = len(self.famName)
  190. self.famList.append("F" + str(famidx + 1))
  191. self.famID.append(cols[0])
  192. self.famName.append(fam)
  193. row = []
  194. self.fam2Path.append(row)
  195. for path in cols[2:]:
  196. # note: a line could have multiple subsytems??
  197. if path[:4] == "CBSS":
  198. continue # skip the clustering-based subsystems
  199. if path in self.pathName:
  200. pathidx = self.pathName.index(path)
  201. else:
  202. pathidx = len(self.pathName)
  203. self.pathList.append("S" + str(pathidx + 1))
  204. self.pathName.append(path)
  205. row = []
  206. self.path2Fam.append(row)
  208. if pathidx not in self.fam2Path[famidx]:
  209. self.fam2Path[famidx].append(pathidx)
  210. if famidx not in self.path2Fam[pathidx]:
  211. self.path2Fam[pathidx].append(famidx)
  212. file.close()
  213. self.pathTot = len(self.pathList)
  214. self.famTot = len(self.famList)
  215. print("total SEED subsystem=%d" % self.pathTot)
  216. print("total SEED functions(families)=%d" % self.famTot)
  218. #read KEGG pathways from ~/pathway/map-title.tab
  219. def ReadKEGGPath(self, pathfile):
  220. try:
  221. file = open(pathfile, "rt")
  222. except IOError:
  223. sys.exit("open file error " + pathfile)
  226. for aline in file:
  227. aline = aline[:-1]
  228. row = aline.split("\t")
  229. self.pathList.append(row[0])
  230. self.pathName.append(row[1])
  231. row = []
  232. self.path2Fam.append(row)
  233. file.close()
  235. self.pathTot = len(self.pathList)
  236. print("total KEGG pathway=%d" % self.pathTot)
  238. #read the KEGG families (KO) from ~/genes/ko
  239. def ReadKO(self, kofile = "", ifreadgene = False, ifgivenspe = ""):
  240. try:
  241. file = open(kofile, "rt")
  242. except IOError:
  243. print("open file %s error" % kofile)
  244. print("read kofile=%s" % kofile)
  245. for aline in file:
  246. aline = aline.strip()
  247. m = re.search(r'^ENTRY\s+(?P<ko>[\S]+)', aline)
  248. if m:
  249. self.famList.append(m.group('ko'))
  250. koidx = len(self.famList) - 1
  251. row = []
  252. self.fam2Path.append(row)
  253. for aline in file:
  254. name = aline[12:-1]
  255. self.famName.append(name)
  256. break
  257. #print "ko=%d %s name=%s" % (koidx, m.group('ko'), name)
  258. continue
  259. m = re.search(r'\[PATH:ko(?P<path>[^\]]+)', aline)
  260. if m:
  261. thispath = m.group('path')
  262. if thispath in self.pathList:
  263. pathidx = self.pathList.index(thispath)
  264. #print "thispath=%s %d idx=%d" % (thispath, pathidx, len(self.famList))
  265. self.fam2Path[koidx].append(pathidx)
  266. self.path2Fam[pathidx].append(koidx)
  267. continue
  269. #this information is only needed for KEGG pathway inference (blast-result to ko assignment)
  270. #reading this information is time-consuming
  271. if not ifreadgene:
  272. continue
  273. m = re.search(r'^GENES', aline)
  274. if not m:
  275. continue
  276. #raw_input(" continue with reading gene...")
  277. lines = [aline]
  278. for aline in file:
  279. if aline[:3] == "///":
  280. break
  281. lines.append(aline)
  282. ifvalid = False
  283. for aline in lines:
  284. #print 'now check line', aline
  285. if aline[15] == ':':
  286. org = aline[12:15].lower()
  287. #print "org", org, "ifgivenspe", ifgivenspe
  288. if ifgivenspe != "" and org != ifgivenspe:
  289. ifvalid = False
  290. elif (ifgivenspe != "" and org == ifgivenspe) or (ifgivenspe == ""):
  291. ifvalid = True
  292. if org in self.orgList:
  293. orgidx = self.orgList.index(org)
  294. else:
  295. orgidx = len(self.orgList)
  296. self.orgList.append(org)
  297. row = []
  298. self.orgGeneList.append(row)
  299. row = []
  300. self.orgGene2Fam.append(row)
  301. if not ifvalid:
  302. continue
  303. #else: the org is the same
  304. info = aline[17:]
  305. info2 = re.sub(r'\([^\)]+\)', "", info)
  306. items = info2.split()
  307. for aquery in items:
  308. #thisgene = org + ":" + aquery
  309. thisgene = aquery
  310. #print "thisgene = ", thisgene
  311. if thisgene in self.orgGeneList[orgidx]:
  312. geneidx = self.orgGeneList[orgidx].index(thisgene)
  313. else:
  314. geneidx = len(self.orgGeneList[orgidx])
  315. self.orgGeneList[orgidx].append(thisgene)
  316. row = []
  317. self.orgGene2Fam[orgidx].append(row)
  318. self.orgGene2Fam[orgidx][geneidx].append(koidx)
  320. file.close()
  321. self.famTot = len(self.famList)
  322. self.famID = self.famList
  323. self.orgTot = len(self.orgList)
  324. print("total KEGG fam=%d" % (self.famTot))
  325. if ifreadgene:
  326. print("total organisms involved =%d" % (self.orgTot))
  327. one2one = 0
  328. one2mul = 0
  329. for i in range(self.orgTot):
  330. #print " org %s has %d genes assigned to KO" % (self.orgList[i], len(self.orgGeneList[i]))
  331. for j in range(len(self.orgGeneList[i])):
  332. if len(self.orgGene2Fam[i][j]) > 1:
  333. one2mul += 1
  334. else:
  335. one2one += 1
  336. print("total %d genes matched to multiple KO; %d matched to single KO" % (one2mul, one2one))
  338. #calcualte the uniqueness of Fam (KEGG families or SEED families)
  339. def CheckUniqueFam(self):
  340. for i in range(self.famTot):
  341. if len(self.fam2Path[i]) > 10:
  342. print("fam=%d %s [%s] map-to-path=%d" % (i, self.famList[i], self.famName[i], len(self.fam2Path[i])))
  343. for p in self.fam2Path[i]:
  344. print(" path-%d[%s %s]" % (p, self.pathList[p], self.pathName[p]))
  345. ubifam = 0
  346. for i in range(self.famTot):
  347. if len(self.fam2Path[i]) > 1:
  348. ubifam += 1
  349. print("total families that mapped to more than one pathway = %d" % ubifam)
  351. for p in range(self.pathTot):
  352. row = []
  353. totfam = len(self.path2Fam[p])
  354. uniquefam = 0
  355. print("pathway-%d[%s; %s] fam=%d" % (p, self.pathList[p], self.pathName[p], totfam))
  356. for k in range(totfam):
  357. fam = self.path2Fam[p][k]
  358. if len(self.fam2Path[fam]) == 1:
  359. uniquefam = uniquefam + 1
  360. row.append(fam)
  361. print(" unique fam-%d %s %s" % (fam, self.famList[fam], self.famName[fam]))
  362. self.path2FamUni.append(row)
  363. print(">>>pathway-%d[%s; %s] fam=%d unique-fam=%d" % (p, self.pathList[p], self.pathName[p], totfam, uniquefam))
  364. def GetPath2FamUniMapped(self, apath, what):
  365. if apath in self.pathList:
  366. p = self.pathList.index(apath)
  367. famlist = []
  368. for fam in self.path2FamUni[p]:
  369. if fam in self.famMapped:
  370. if what == "name":
  371. famlist.append(self.famList[fam])
  372. else:
  373. famlist.append(fam)
  374. return famlist
  375. else:
  376. return []
  378. def GetPath2FamMapped(self, apath, what):
  379. if apath in self.pathList:
  380. p = self.pathList.index(apath)
  381. famlist = []
  382. #print "apath=", apath, "total fam", len(self.path2Fam[p])
  383. for fam in self.path2Fam[p]:
  384. #print " >>>check fam", fam, "famMapped-total", len(self.famMapped)
  385. if fam in self.famMapped:
  386. if what == "name":
  387. famlist.append(self.famList[fam])
  388. else:
  389. famlist.append(fam)
  390. #print " >>>Found in the famMapped"
  391. return famlist
  392. else:
  393. return []
  395. #return the index of families
  396. def GetPath2FamUni(self, apath):
  397. if apath in self.pathList:
  398. p = self.pathList.index(apath)
  399. return self.path2FamUni[p]
  400. else:
  401. return []
  402. #return the index of families
  403. def GetPath2Fam(self, apath):
  404. if apath in self.pathList:
  405. p = self.pathList.index(apath)
  406. return self.path2Fam[p]
  407. else:
  408. return []
  410. #note: this function only works when the givenspe is defined (see KEGG2html.py)
  411. def OrthMapBasedOnKO(self, spe=""):
  412. if spe == "":
  413. return
  414. if spe not in self.orgList:
  415. return
  416. self.famMapped = []
  417. s = self.orgList.index(spe)
  418. print("spe", spe, "total gene", len(self.orgGeneList[s]))
  419. for g in range(len(self.orgGeneList[s])):
  420. for fam in self.orgGene2Fam[s][g]:
  421. if fam not in self.famMapped:
  422. self.famMapped.append(fam)
  423. print("total family=", len(self.famList), "total mapped=", len(self.famMapped))
  424. #raw_input("type enter to continue")
  426. def OrthMap(self, famidxlist=[], famnamelist=[], famcount = []):
  427. if len(famidxlist) == 0 and len(famnamelist) == 0:
  428. return []
  429. if famcount:
  430. self.famCount = [0] * self.famTot
  431. #get only the orthologs that are mappped to a pathway
  432. if len(famidxlist) > 0:
  433. famlist = famidxlist
  434. famref = self.famList
  435. else:
  436. famlist = famnamelist
  437. famref = self.famName
  438. orthtot0 = len(famlist)
  439. orthtotfind = 0
  440. orthtotmap = 0
  441. self.famMapped = []
  442. pathmap = [0] * self.pathTot
  443. for i in range(len(famlist)):
  444. orth = famlist[i]
  445. if orth in famref:
  446. idx = famref.index(orth)
  447. if famcount:
  448. self.famCount[idx] = famcount[i]
  449. orthtotfind += 1
  450. if len(self.fam2Path[idx]) > 0:
  451. self.famMapped.append(idx)
  452. orthtotmap += 1
  453. for path in self.fam2Path[idx]:
  454. pathmap[path] = 1
  455. print("original ortholog=%d found-in-the-fam-list=%d found-in-the-fam-mapped-to-pathway=%d" % (orthtot0, orthtotfind, orthtotmap))
  456. self.pathMapped = []
  457. for p in range(self.pathTot):
  458. if pathmap[p]:
  459. self.pathMapped.append(p)
  461. #assign orthologs to pathways
  462. #strategy 1: first assign unique ones -- then other orthologs
  463. def Orth2PathUni(self, famidxlist=[], famnamelist=[], famcount=[]):
  464. self.OrthMap(famidxlist = famidxlist, famnamelist = famnamelist, famcount=famcount)
  465. orthtotmap = len(self.famMapped)
  466. #sort the orthologs based on their "uniqueness"
  467. fam2path = []
  468. for i in self.famMapped:
  469. if len(self.fam2Path[i]) == 0:
  470. continue
  471. fam2path.append((len(self.fam2Path[i]), i))
  472. #print "fam2path = ", len(fam2path)
  473. #raw_input("type enter to continue..")
  475. fam2pathsorted = sorted(fam2path, key=operator.itemgetter(0))
  476. pathsort = map(operator.itemgetter(0), fam2pathsorted)
  477. famsort = map(operator.itemgetter(1), fam2pathsorted)
  479. #for i in range(len(famsort)):
  480. # print "fam0 %d fam %d [%s; %s] topath %d" % (i, famsort[i], self.famList[famsort[i]], self.famName[famsort[i]], pathsort[i])
  482. #pathfam & pathfam0: the number of fam families assigned to each pathway
  483. pathfam = [0] * self.pathTot
  484. pathfam0 = [0] * self.pathTot
  486. #pathfam0: the number of fam assigned to each pathway (using all multiple assignments)
  487. for fam in famsort:
  488. for p in self.fam2Path[fam]:
  489. pathfam0[p] = pathfam0[p] + 1
  491. #pathfam: the number of fam assigned to each pathway considering the "uniqueness" of fam to each pathway
  492. maxhit = pathsort[-1]
  493. print("the maximum number of pathways a family is assigned to=%d" % maxhit)
  494. hit = 1
  495. unassigned = len(famsort)
  496. beg = 0
  497. annpath = []
  498. famassign = [-1] * orthtotmap
  499. while (hit <= maxhit) and (unassigned > 0):
  500. #print "check hit=%d beg=%d" % (hit, beg)
  501. for k in range(beg, orthtotmap):
  502. if famassign[k] != -1:
  503. continue
  504. if pathsort[k] > hit:
  505. break
  506. fam = famsort[k]
  507. maxsaturate = -1
  508. maxsaturate_p = 0
  509. #print "check k=%d fam=%d %s %s" % (k, fam, self.famList[fam], self.famName[fam])
  510. for p in self.fam2Path[fam]:
  511. saturate = 1.0 * pathfam[p] / len(self.fam2Path[fam])
  512. if(saturate > maxsaturate):
  513. maxsaturate = saturate
  514. maxsaturate_p = p
  515. famassign[k] = maxsaturate_p
  516. pathfam[maxsaturate_p] = pathfam[maxsaturate_p] + 1
  517. beg = k
  519. unassigned = 0
  520. for k in range(orthtotmap):
  521. if famassign[k] == -1:
  522. unassigned = unassigned + 1
  523. #print "try hit=%d unassigned=%d (tot=%d)" % (hit, unassigned, orthtotmap)
  524. #raw_input()
  525. hit = hit + 1
  527. annpath0 = 0
  528. annpath = 0
  529. self.pathMappedOpt = []
  530. for k in range(self.pathTot):
  531. if pathfam0[k] != 0:
  532. annpath0 = annpath0 + 1
  533. if pathfam[k] != 0:
  534. annpath = annpath + 1
  535. self.pathMappedOpt.append(k)
  537. print("total pathway %d (%d) is found, compared to %d (%d)" % (annpath, len(self.pathMappedOpt), annpath0, len(self.pathMapped)))
  538. print("%-50s %s\t%s" % ("#pathway", "fam-assigned(all)", "fam-assigned(unique)[weight]"))
  539. for p in range(self.pathTot):
  540. if pathfam0[p] == 0 and pathfam[p] == 0:
  541. continue
  542. tmp = self.pathList[p] + "[" + self.pathName[p] + "]"
  543. weight = .0
  544. for k in range(orthtotmap):
  545. ks = famsort[k]
  546. if famassign[k] != p:
  547. continue
  548. weight = weight + 1.0 / len(self.fam2Path[ks])
  549. print("%-50s %d\t%d[%.1f]" % (tmp, pathfam0[p], pathfam[p], weight))
  550. return self.pathMappedOpt
  552. #Parsinomy approach to pathway inference
  553. def Orth2PathMin(self, famidxlist=[], famnamelist=[], famcount=[], mpsfile="test.mps", glpsol=""):
  554. # write mps file (the input for glpsol, the integer programming package)
  555. print("now write mps file..")
  556. self.WriteMps(famidxlist=famidxlist, famnamelist=famnamelist, famcount=famcount, mpsfile=mpsfile)
  558. # run glpsol
  559. global glpsol0
  560. if glpsol == "":
  561. glpsol = glpsol0
  562. lpout = mpsfile + ".LPout"
  563. # LJM change to subprocess call
  564. # command = glpsol + " " + mpsfile + " -o " + lpout
  565. command = [glpsol,mpsfile,"-o",lpout]
  566. #print "now run command = %s" % command
  567. #os.system(command)
  568. try:
  569. subprocess_output=subprocess.check_output(command)
  570. except (EnvironmentError, subprocess.CalledProcessError) as e:
  571. message="Error when running glpsol from MinPath.\n"
  572. if hasattr(e, 'output') and e.output:
  573. message+="\nError message returned from glpsol :\n" + e.output.decode("utf-8") +"\n"
  574. sys.exit(message)
  575. # check the result
  576. self.GetLPOut(lpout)
  578. return self.pathMappedOpt
  580. #output mps file for integer programming (most parsinomy pathway inference)
  581. def WriteMps(self, famidxlist=[], famnamelist=[], famcount=[], mpsfile="test.mps"):
  582. try:
  583. file = open(mpsfile, "w")
  584. except IOError:
  585. sys.exit("open file error " + mpsfile)
  587. str = "%-14s%s\n" % ("NAME", "PATH")
  588. file.write(str)
  590. self.OrthMap(famidxlist=famidxlist, famnamelist=famnamelist, famcount=famcount)
  591. orthtotmap = len(self.famMapped)
  593. #write ROWS
  594. file.write("ROWS\n")
  595. file.write(" N NUM\n")
  596. for orth in self.famMapped:
  597. str = " G F%s\n" % self.famList[orth];
  598. #note 1: use a different idx of family for mps file
  599. #note 2: when use E, there is no feasible solution
  600. #G>=1, mean each family has to be assigned to at least one pathway
  601. file.write(str)
  603. #write COLUMNS
  604. #the same column (pathway) needs to be organized in the same block
  605. file.write("COLUMNS\n")
  606. pathvalid = [0] * self.pathTot
  607. for p in self.pathMapped:
  608. #note: use a different pathway idx in mps
  609. pathname = "P%s" % self.pathList[p]
  610. str = " %-10s%-10s%10d\n" %(pathname, "NUM", 1)
  611. file.write(str)
  612. for orth in self.famMapped:
  613. famname = "F%s" % self.famList[orth];
  614. for path in self.fam2Path[orth]:
  615. if path == p:
  616. str = " %-10s%-10s%10d\n" %(pathname, famname, 1)
  617. file.write(str)
  618. pathvalid[p] = 1
  620. #write RHS
  621. file.write("RHS\n")
  622. for orth in self.famMapped:
  623. famname = "F%s" % self.famList[orth]
  624. str = " %-10s%-10s%10.1f\n" % ("RHS1", famname, 1.0);
  625. file.write(str)
  627. #write bounds
  628. file.write("BOUNDS\n")
  629. for p in range(self.pathTot):
  630. if pathvalid[p]:
  631. path = self.pathList[p]
  632. pathname = "P%s" % path;
  633. str = " BV %-10s%-10s\n" %("BND1", pathname);
  634. #all variants are binary (1 keep the pathway; 0 pathway not necessary)
  635. file.write(str)
  637. file.write("ENDATA\n")
  638. file.close()
  640. print("End of PrintMPS")
  642. def GetLPOut(self, lpoutfile="test.mps.LPout"):
  643. try:
  644. file = open(lpoutfile, "rt")
  645. except IOError:
  646. sys.exit("open file error " + lpoutfile)
  649. keeppath = []
  650. for aline in file:
  651. aline = aline.strip()
  652. cols = aline.split()
  653. if len(cols) < 2:
  654. continue
  655. if cols[0] == "Columns:":
  656. Columns = int(cols[1])
  657. elif cols[0] == "Objective:":
  658. MINimum = int(cols[3])
  659. elif cols[0] == "No." and cols[1] == "Column":
  660. for aline2 in file:
  661. if aline2[0] == '-':
  662. continue
  663. aline2 = aline2.strip()
  664. cols2 = aline2.split()
  665. if len(cols2) < 1:
  666. break
  667. if cols2[3] == '1':
  668. keeppath.append(cols2[1][1:])
  669. #check with WriteMps: the pathway idx used in mps is to add "P" before the pathList
  670. file.close()
  671. if len(keeppath) != MINimum:
  672. print("reading %s error: minimum %d read %d" % (lpoutfile, MINimum, len(keeppath)))
  673. sys.exit()
  675. self.pathMappedOpt = []
  676. for path in keeppath:
  677. if path not in self.pathList:
  678. print("Error: unknown pathList %s" % path)
  679. sys.exit()
  680. pathidx = self.pathList.index(path)
  681. self.pathMappedOpt.append(pathidx)
  683. print("total pathways mappd: before inference %d, after inference %d" % (len(self.pathMapped), len(self.pathMappedOpt)))
  685. #add the pathways with many functions annotated, even they were considered as redundant ones!
  686. def PopulatePath(self, pathmapped = [], par = 0.7):
  687. famvalid = [0] * self.famTot
  688. for fam in self.famMapped:
  689. famvalid[fam] = 1
  691. addpath = 0
  692. for p in range(self.pathTot):
  693. if len(self.path2Fam[p]) == 0:
  694. continue
  695. if not p in pathmapped:
  696. add = 0
  697. for f in self.path2Fam[p]:
  698. if famvalid[f] == 1:
  699. add += 1
  700. #pathways with most functions annotated should be added back -- even it is a redundant one
  701. print("pathway", p, self.pathList[p], self.pathName[p], "path2fam", len(self.path2Fam[p]), " real-family", add)
  702. if add >= len(self.path2Fam[p]) * par:
  703. pathmapped.append(p)
  704. addpath += 1
  705. print("this pathway is added back")
  706. #else:
  707. # print "this pathway does not have enough functions"
  708. #raw_input("type enter to continue")
  710. print("added pathway =", addpath)
  712. #remove the pathways with too few functions annotated (e.g., 2, use par),
  713. #even when their associated families are annotated(but NOT the unique ones)
  714. #not unique families assigned to this pathway? ubiquitous families have to be assigned to at least one of the pathways, right
  715. def RemoveSparsePath(self, pathmapped = [], par = 2):
  716. famvalid = [0] * self.famTot
  717. for fam in self.famMapped:
  718. famvalid[fam] = 1
  720. delpath = 0
  721. for p in range(self.pathTot):
  722. if len(self.path2Fam[p]) == 0:
  723. continue
  724. if p in pathmapped:
  725. add = 0
  726. uni = 0
  727. for f in self.path2Fam[p]:
  728. if famvalid[f] == 1:
  729. add += 1
  730. if len(self.fam2Path[f]) == 1:
  731. uni += 1
  732. #pathways with few functions annotated are removed
  733. if uni == 0 and add <= par:
  734. pathmapped.remove(p)
  735. delpath += 1
  736. print("pathway", p, self.pathList[p], self.pathName[p], "path2fam", len(self.path2Fam[p]), " real-family", add, " is removed from the list!!")
  737. #raw_input("type enter to continue")
  739. print("deleted pathway =", delpath)
  741. def DiffPathMap(self, maps, tags):
  742. maps.insert(0, self.pathMapped)
  743. tags.insert(0, "Ori")
  744. mapnum = len(maps)
  745. pathvalid = intmatrix(self.pathTot, mapnum)
  746. for m in range(mapnum):
  747. for p in maps[m]:
  748. pathvalid[p][m] = 1
  749. print("#Summary for the pathway inference")
  750. #print description line
  751. str = "%-5s %-10s %-70s %-5s %-5s" % ("ID", "List", "Name", "Fam", "Fam-found")
  752. for atag in tags:
  753. str += " %-3s" % atag
  754. print(str + " Same/Diff")
  755. #print each pathway
  756. totsame = 0
  757. totdiff = 0
  758. famvalid = [0] * self.famTot
  759. for fam in self.famMapped:
  760. famvalid[fam] = 1
  762. for p in range(self.pathTot):
  763. add = sum(pathvalid[p])
  764. if add == 0:
  765. continue
  766. add = sum(pathvalid[p][1:])
  767. if add == mapnum - 1 or add == 0:
  768. label = "Same"
  769. if add != 0:
  770. totsame += 1
  771. else:
  772. label = "Diff"
  773. totdiff += 1
  774. add = 0
  775. for f in self.path2Fam[p]:
  776. if famvalid[f] == 1:
  777. add += 1
  778. str = "%-5d %-10s %-70s %-5d %-5d" % (p + 1, self.pathList[p], self.pathName[p], len(self.path2Fam[p]), add)
  779. for m in range(len(maps)):
  780. str += " %-3d" % pathvalid[p][m]
  781. print(str + " " + label)
  782. #print total number line
  783. str = "%-5s %-10s %-70s %-5s %-5s" % ("#total", "", "", "", "")
  784. for m in range(mapnum):
  785. str += " %-3d" % len(maps[m])
  786. print(str)
  787. #print functional diveristy line
  788. #str = "#functional-diversity [max: log(%d)=%.3f]" % (self.pathTot, math.log(self.pathTot * 1.0))
  789. #str = "%-99s" % str
  790. #for m in range(mapnum):
  791. ## str += " %.3f" % math.log(len(maps[m]) * 1.0)
  792. #print str
  793. print("#total match=%d diff=%d" % (totsame, totdiff))
  795. def WriteReport(self, minpath, reportfile, detailfile):
  796. na = True
  797. if self.whichDB == "KEGG":
  798. keggmap = []
  799. keggdir = "/dataomics/kegg/kegg-curr"
  800. mapfile = keggdir + "/pathway/" + self.speID.lower() + "/map.list"
  801. if os.path.exists(mapfile):
  802. file = open(mapfile, "rt")
  803. for aline in file:
  804. m = re.match('^[^\d]+(?P<id>\d+)', aline)
  805. if m:
  806. id = m.group('id')
  807. idx = self.pathList.index(id)
  808. keggmap.append(idx)
  809. na = False
  810. tags = ["kegg", "naive", "minpath"]
  811. maps = [keggmap, self.pathMapped, minpath]
  812. else:
  813. seedmap = []
  814. if self.whichDB == 'SEED':
  815. tags = ["seed", "naive", "minpath"]
  816. else:
  817. tags = ["any", "naive", "minpath"]
  818. maps = [seedmap, self.pathMapped, minpath]
  819. mapnum = len(maps)
  820. pathvalid = intmatrix(self.pathTot, mapnum)
  821. for m in range(mapnum):
  822. for p in maps[m]:
  823. pathvalid[p][m] = 1
  824. famvalid = [0] * self.famTot
  825. for fam in self.famMapped:
  826. famvalid[fam] = 1
  828. file = open(reportfile, "w")
  829. if detailfile:
  830. detail = open(detailfile, "w")
  831. for p in range(self.pathTot):
  832. add = sum(pathvalid[p])
  833. if add == 0:
  834. continue
  835. add = 0
  836. for f in self.path2Fam[p]:
  837. if famvalid[f] == 1:
  838. add += 1
  839. if na:
  840. tmp = "n/a"
  841. else:
  842. tmp = pathvalid[p][0]
  843. file.write(get_string("path", self.pathList[p], tags[0], tmp, " naive", pathvalid[p][1], " minpath", pathvalid[p][2], " fam0 ", len(self.path2Fam[p]), " fam-found ", add, " name ", self.pathName[p])+"\n")
  845. if not (detailfile and pathvalid[p][2]):
  846. continue
  847. #print details
  848. detail.write(get_string("path", self.pathList[p], "fam0", len(self.path2Fam[p]), "fam-found", add, "#", self.pathName[p])+"\n")
  849. for f in self.path2Fam[p]:
  850. if famvalid[f] == 1 and self.famCount:
  851. detail.write(get_string(" ", self.famID[f], "hits", self.famCount[f], "#", self.famName[f])+"\n")
  852. elif famvalid[f] == 1:
  853. detail.write(get_string(" ", self.famID[f], "#", self.famName[f])+"\n")
  855. print("")
  856. print("Results are saved in file:" + reportfile)
  857. file.close()
  858. if detailfile:
  859. print("Details are saved in file:" + detailfile)
  860. detail.close()
  862. # this function reads in KO/fig assignment, then map KO/fig families to the pathways
  863. # last update by Yuzhen Ye on July 3, 2009
  864. def Orth2Path(infile = "demo.ko", whichdb = "KEGG", mpsfile = "test.mps", reportfile = "test.minpath", detailfile = "", mapfile=""):
  865. try:
  866. file = open(infile, "rt")
  867. except IOError:
  868. sys.exit("open file error " + infile)
  871. orthlist, orthcount = [], []
  872. add = 0
  873. for aline in file:
  874. #aline = aline.strip()
  875. #tmp = aline.split("\t")
  876. tmp = aline.strip().split()
  877. if len(tmp) >= 2:
  878. try:
  879. ab = float(tmp[1])
  880. except (ValueError,IndexError):
  881. ab = 0.0
  882. add = add + ab
  883. if tmp[0] not in orthlist:
  884. orthlist.append(tmp[0])
  885. orthcount.append(ab)
  886. #print "ko-%d=%s" % (len(orthlist), tmp[1])
  887. else:
  888. idx = orthlist.index(tmp[0])
  889. orthcount[idx] += ab
  890. file.close()
  892. print("total input orth=%d unique=%d" % (add, len(orthlist)))
  894. test = MinPath(whichdb = whichdb, mapfile = mapfile) #default pathwaydb: KEGG
  896. if whichdb == "KEGG":
  897. map = test.Orth2PathMin(famidxlist=orthlist, famnamelist=[], famcount=orthcount, mpsfile=mpsfile)
  898. elif whichdb == "SEED":
  899. map = test.Orth2PathMin(famidxlist=[], famnamelist=orthlist, famcount=orthcount, mpsfile=mpsfile)
  900. else:
  901. map = test.Orth2PathMin(famidxlist=[], famnamelist=orthlist, famcount=orthcount, mpsfile=mpsfile)
  902. #KEGG by ids, and fig by names
  904. map_add = map[:]
  905. par = 0.5
  906. test.PopulatePath(pathmapped = map_add, par = par)
  908. test.WriteReport(map_add, reportfile, detailfile)
  910. os.system("rm " + mpsfile + "*")
  912. if __name__ == '__main__':
  913. kofile, figfile, anyfile, mapfile, mpsfile, reportfile, detailfile = "", "", "", "", "test.mps", "test.minpath", ""
  914. for i in range(len(sys.argv)):
  915. if sys.argv[i] == "-ko":
  916. kofile = sys.argv[i + 1]
  917. elif sys.argv[i] == "-fig":
  918. figfile = sys.argv[i + 1]
  919. elif sys.argv[i] == "-any":
  920. anyfile = sys.argv[i + 1]
  921. elif sys.argv[i] == "-map":
  922. mapfile = sys.argv[i + 1]
  923. elif sys.argv[i] == "-report":
  924. reportfile = sys.argv[i + 1]
  925. elif sys.argv[i] == "-details":
  926. detailfile = sys.argv[i + 1]
  927. elif sys.argv[i] == "-mps":
  928. mpsfile = sys.argv[i + 1]
  929. if kofile:
  930. Orth2Path(infile = kofile, mpsfile = mpsfile, reportfile = reportfile, detailfile = detailfile)
  931. elif figfile:
  932. Orth2Path(infile = figfile, mpsfile = mpsfile, reportfile = reportfile, detailfile = detailfile, whichdb = "SEED")
  933. elif anyfile and mapfile:
  934. Orth2Path(infile = anyfile, mpsfile = mpsfile, reportfile = reportfile, detailfile = detailfile, whichdb = "ANY", mapfile=mapfile)
  935. else:
  936. print("Usage: python MinPath.py <-ko filename>/<-fig filename>/<-any annfile> [-map mapfile] [-report filename] [-details detailed-output]")
  937. print("Note: your input file can contain functional annotations in either of the following")
  938. print(" -ko file: annotation in KEGG KO families")
  939. print(" -fig file: annotation in SEED fig families")
  940. print(" -any file: annotation in any families, then you must specify -map, the pathway-function mapping file")
  941. print("Example 1: python MinPath.py -ko demo.ko -report demo.ko.minpath")
  942. print("Example 2: python MinPath.py -ko demo.ko -report demo.ko.minpath -details demo.ko.minpath.details")
  943. print("Example 3: python MinPath.py -fig demo.fig -report demo.fig.minpath")
  944. print("Example 4: python MinPath.py -fig demo.fig -report demo.fig.minpath -details demo.fig.minpath.details")
  945. print("Example 5: python MinPath.py -any demo.ec -map ec2path -report demo.ec.minpath -details demo.ec.minpath.details")
  946. sys.exit(1)

MinPath12hmp.py at commit d91caaa, under GPL-3.0 · at the source

Overview

Authors: Xin Xue1, Lin-Ying Luo1, Jing Wang2, Rui Yang2, Xiao-Hui Ma2, Gen-Bei Wang2, Zhao-Hui Song2, Xin-Xin Li2
  1. School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
  2. National Key Laboratory of Chinese Medicine Modernization, Tasly Research Academy, Tasly Holding Group Co, Ltd., Tianjin, China
Institutions: China Pharmaceutical University (China); Tasly Holding Group (China) (China)
Journal: Frontiers in physiology, volume 17, article 1827824
Dates: received 11 March 2026; accepted 29 May 2026; published online 17 June 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.3389/fphys.2026.1827824 · PMID 42389750 · PMCID PMC13318577 · OpenAlex W7164880331
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: rat (organism), other condition (population), cellular / molecular (subfield)
Methods: Statistics, Machine learning, Connectivity
Keywords: immune mechanism, intestinal flora, microbial-gut-brain axis, Shao-Ma-Zhi-Jing granules, Tourette syndrome
Topic: Obsessive-Compulsive Spectrum Disorders (Clinical Psychology, Psychology), according to OpenAlex
Citations: not cited yet (Europe PMC); 53 references in the paper

Abstract

Introduction: Shao-Ma-Zhi-Jing Granules (SMZJ) is clinically used for Tourette syndrome (TS). This study aimed to investigate the regulatory effects of SMZJ on the immune system and gut microbiota of the 3,3’-iminodipropionitrile (IDPN)-induced TS rat model.

Methods: Immune-related indicators were detected by flow cytometry, western blotting, ELISA and qRT-PCR. Gut microbiota composition was analyzed via 16S rDNA sequencing, and Spearman analysis was performed to assess the correlation between gut microbiota and immune function.

Results: SMZJ suppressed IDPN-induced stereotypical behaviors. Furthermore, SMZJ regulated the mRNA and protein levels of T helper 1 (Th1), Th2, Th17, and T regulatory (Treg) cell-related transcription factors and modulated Th1 and Th2 cytokines in the TS rat model. SMZJ downregulated the inflammatory pathway in the brain striatum, the TNF-α and IL-6 (inflammatory cytokines) levels, and the striatal iNOS levels in the TS rat model. The diversity and structure of the gut microbiota were remodeled using the SMZJ-treated TS rat model. SMZJ modulated the correlation between immune parameters and gut microbiota.

Conclusions: SMZJ alleviated peripheral and neuroinflammation in TS rats via promoting T cell differentiation and downregulating TNF-α and IL-6 levels, which may be related to changes in the cAMP/PI3K/Akt/NF-κB signaling pathway. SMZJ downregulated the activation of striatal M1 microglia in the TS model. SMZJ may potentially modulated gut microbiota structure and metabolism, relieves peripheral and neuroinflammation, and ameliorates intestinal mucosal barrier injury.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above.

picrust/picrust2

License: GPL-3.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: d91caaa287444a79161023f7bf1547202b7acd64, 25 September 2026
Languages: Python (33), R (2)
Size: 211 files, 35 scripts
Software Heritage: archived
Found in: the text, “Analysis of gut microbiota using 16S rRNA sequen”
Holds: README, license file, environment (pyproject.toml, setup.py), tests, continuous integration
Not found: CITATION.cff, documentation
Tools: pandas (10 files), NumPy (5 files), h5py (1 file), SciPy (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
37 files
At the source: github.com/picrust/picrust2

Tracing map

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Data

Datasets cited

Data availability statement

The data presented in the study are deposited in the Mendeley Data repository, accession number https://doi.org/10.17632/246p9b4tp4.1.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

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Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, pages, dates, 8 authors, 5 keywords, 52 references.

Cite

This paper

Xue, X., Luo, L.-Y., Wang, J., Yang, R., Ma, X.-H., Wang, G.-B., Song, Z.-H., & Li, X.-X. (2026). Shao-Ma-Zhi-Jing granules alleviate Tourette Syndrome by modulating the cAMP/PI3K/AKT/NF-κB signaling pathway, T cell differentiation, microglia, and gut microbiota. Frontiers in physiology, 17, 1827824. https://doi.org/10.3389/fphys.2026.1827824

BibTeX

@article{xue2026shao,
author = {Xue, Xin and Luo, Lin-Ying and Wang, Jing and Yang, Rui and Ma, Xiao-Hui and Wang, Gen-Bei and Song, Zhao-Hui and Li, Xin-Xin},
title = {{Shao-Ma-Zhi-Jing granules alleviate Tourette Syndrome by modulating the cAMP/PI3K/AKT/NF-κB signaling pathway, T cell differentiation, microglia, and gut microbiota}},
journal = {Frontiers in physiology},
year = {2026},
month = jun,
volume = {17},
pages = {1827824},
publisher = {Frontiers Media SA},
issn = {1664-042X},
doi = {10.3389/fphys.2026.1827824},
url = {https://doi.org/10.3389/fphys.2026.1827824},
pmid = {42389750},
pmcid = {PMC13318577}
}

RIS

TY - JOUR
AU - Xue, Xin
AU - Luo, Lin-Ying
AU - Wang, Jing
AU - Yang, Rui
AU - Ma, Xiao-Hui
AU - Wang, Gen-Bei
AU - Song, Zhao-Hui
AU - Li, Xin-Xin
TI - Shao-Ma-Zhi-Jing granules alleviate Tourette Syndrome by modulating the cAMP/PI3K/AKT/NF-κB signaling pathway, T cell differentiation, microglia, and gut microbiota
T2 - Frontiers in physiology
J2 - Front Physiol
PY - 2026
DA - 2026/06/17
VL - 17
SP - 1827824
SN - 1664-042X
PB - Frontiers Media SA
DO - 10.3389/fphys.2026.1827824
UR - https://doi.org/10.3389/fphys.2026.1827824
LA - en
ER -

CSL-JSON

{
"id": "10.3389/fphys.2026.1827824",
"type": "article-journal",
"title": "Shao-Ma-Zhi-Jing granules alleviate Tourette Syndrome by modulating the cAMP/PI3K/AKT/NF-κB signaling pathway, T cell differentiation, microglia, and gut microbiota",
"container-title": "Frontiers in physiology",
"author": [
{
"family": "Xue",
"given": "Xin"
},
{
"family": "Luo",
"given": "Lin-Ying"
},
{
"family": "Wang",
"given": "Jing"
},
{
"family": "Yang",
"given": "Rui"
},
{
"family": "Ma",
"given": "Xiao-Hui"
},
{
"family": "Wang",
"given": "Gen-Bei"
},
{
"family": "Song",
"given": "Zhao-Hui"
},
{
"family": "Li",
"given": "Xin-Xin"
}
],
"container-title-short": "Front Physiol",
"volume": "17",
"page": "1827824",
"DOI": "10.3389/fphys.2026.1827824",
"PMID": "42389750",
"PMCID": "PMC13318577",
"ISSN": "1664-042X",
"publisher": "Frontiers Media SA",
"URL": "https://doi.org/10.3389/fphys.2026.1827824",
"language": "en",
"issued": {
"date-parts": [
[
2026,
6,
17
]
]
}
}

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